ENCODE/Junk DNA Fiasco: The IDiots Don't Like Me

Let's look at how the IDiots are responding to this publicity fiasco. Casey Luskin begins with ...

University of Toronto biochemistry professor Larry Moran is not happy with the results of the ENCODE project, which report evidence of "biochemical functions for 80% of the genome." Other evolution-defenders are trying to dismiss this paper as mere "hype".

Yes that's right -- we're supposed to ignore the intentionally unambiguous abstract of an 18-page Nature paper, the lead out of 30 other simultaneous papers from this project, co-authored by literally hundreds of leading scientists worldwide, because it's "hype." (Read the last two or so pages of the main Nature paper to see the uncommonly long list of international scientists who were involved with this project, and co-authored this paper.) Larry Moran and other vocal Internet evolution-activists are welcome to disagree and protest these conclusions, but it's clear that the consensus of molecular biologists -- people who actually study how the genome works -- now believe that the idea of "junk DNA" is essentially wrong.

I have consistently maintained that the junk DNA debate is a genuine scientific controversy. There are legitimate scientists on both sides of the issue. This often comes up when talking to creationists because they usually claim that the concept of junk DNA is a prediction of Darwinism and all Darwinists believe in it.

I have consistently maintained that there's plenty of evidence for junk DNA and those scientists who dismiss the concept are wrong. In my review of The Myth of Junk DNA I specifically addressed the claims of the ENCODE project based on their 2007 pilot study. See: Junk & Jonathan: Part 6—Chapter 3.

Nothing has changed. The ENCODE consortium scientists were wrong in 2007 and they are still wrong—all of them. Casey Luskin thinks that these scientists are the experts on how the genome works but all the evidence suggests otherwise. It suggests that they haven't really thought about the big picture and about junk DNA. They didn't do their homework in 2007 and they haven't done it since.

Moran, for his part, thinks that all these other scientists aren't just wrong, but that they are misrepresenting the evidence -- with dire consequences for the public scientific debate over evolution. Over on his blog, he's been filling pages with words, pleading with the ENCODE project researchers, and their friends in the media, to tone down their discussions of these results so as not to lend support to intelligent design (or as Moran unendingly puts it, "the creationists").

I would never, ever, try to misrepresent science in order to strengthen the argument against creationism. That's not what's happening here. The science is being misrepresented, in my opinion, and unfortunately the bad science being promoted by the ENCODE consortium plays into the hands of the creationists, especially the Intelligent Design Creationists.

I will fight that by continuing to present evidence that junk DNA exists and that our genome is mostly junk. I will also try to show why the ENCODE results don't say what the consortium claims. Yes, my life is more complicated because of the mistakes made by the ENCODE consortium but it's the science that concerns me, not the IDiots.

Aside from the fact that Larry Moran is very bothered by the prospect that our genome is "full of wonderful sophisticated control elements" and now sees his mission as controlling the "damage" done by scientists talking about that evidence, what else do Moran's words tell us?

First, they show that evolution-activists are susceptible to letting sociopolitical concerns influence their words and behavior. They might treat a study one way, or another because of the feared implications of the evidence, not because of the evidence.

This is not true. Good science trumps all, as far as I'm concerned. If it turns out that almost all of our genome is functional then so be it. I'll be embarrassed as a scientist because I got it wrong. I really don't care very much about the creationists because they are wrong about everything else.

Second, Moran's writing shows that the implications evolutionists fear most are those that lend support to intelligent design (or as they often put it, "the creationists"). They claim their pages and pages of rebuttal-text are simply about enforcing "accuracy," but I suspect Moran et al. wouldn't be so up in arms if there weren't implications here that they fear lend credence to ID. It's not hard to understand why Moran and his colleagues are coming out and forcefully attacking this ENCODE paper.

Right. It's not hard to understand. Unless you're Casey Luskin and you have an agenda.

Third, this shows that many evolutionists would like to believe that the mainstream news media are generally on their "side," and will respond favorably to requests, pleas, and demands to not print statements friendly to intelligent design. Based upon years of personal experience working with the mainstream media, I have to say that this assumption is mostly valid. In this case, however, it seems like folks in the media were largely oblivious to the implications regarding intelligent design, and the fact that ID proponents have been predicting the demise of junk DNA for years. The media certainly haven't mentioned ID at all in the flurry of stories on this paper. These new ENCODE papers, and their coverage in the media, appear to have been driven by the fact that hundreds of leading researchers from around the world are now convinced by massive amounts of data that junk DNA is essentially wrong.

I've been upset with the way the media covers lots of science stories that have no implications for creationists. This is no different. My goal is good science education and scientific literacy.

I admit that if I succeed creationism will die but that's really just a bonus.

So we're left in a situation where evolution-activists are castigating the ENCODE project and the news media for allegedly "overstating" their findings with "hype" because "[t]he creationists are going to love" this research. But we're given no persuasive motive explaining why these scientists and reporters would overstate anything here. If the scientists and reporters allegedly promoting the "hype" are not friendly to intelligent design, what reason would they have to overstate evidence that's friendly to that position? These scientists involved with ENCODE already have all the funding, prestige, and CVs filled with publications that they need.

Does anyone else see the irony here? Prestigious evolutionary biologists have been publishing articles supporting evolution for decades and each time they do so the creationists try to discredit the "Darwinists." The instant a respectable scientist says something that's favorable to the creationists they are all over it. Now the reputation of prestigious scientists is something to be lauded and applauded.

It's called having your cake and eating it too. It's also called hypocrisy.

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Does anyone else see the irony here? Prestigious evolutionary biologists have been publishing articles supporting evolution for decades and each time they do so the creationists try to discredit the "Darwinists." The instant a respectable scientist says something that's favorable to the creationists they are all over it. Now the reputation of prestigious scientists is something to be lauded and applauded.

This one really hits the nail. Interestingly, Luskin and co. are swallowing the ENCODE abstract, hook, line and sinker, no questions asked. However, would anyone care to guess what Luskin and co. will be swallowing uncritically if the scientists of the ENCODE project state that not only did evolution happen, but it was an unguided process that didn't require divine intervention to result in us and our critical faculties? For some strange reason, I think they'll suddenly object.

It's very hard to see how anyone can read the ENCODE papers and take them as evidence against evolution - evolution features prominently in many of those papers, both as a guiding principles and as yet more evidence for it

Prestigious evolutionary biologists have been publishing articles supporting evolution for decades and each time they do so the creationists try to discredit the "Darwinists." The instant a respectable scientist says something that's favorable to the creationists they are all over it. Now the reputation of prestigious scientists is something to be lauded and applauded.

Excellent point. It's the same as when creationists say they don't need evidence for belief in god... until scientists discover something that creationists think counts as evidence, and then they're all over it.

"ENCODE researchers really don't know what they are talking about ..."

Because they designed the experiments, collected the data, interpreted the data, and wrote about it? Kudos to the ENCODE researchers and to all scientists everywhere who are too busy actually doing science to get involved in trivial debates like this one.

And as far as the public goes, well, hate to break it to you, but the public isn't paying nearly as much attention as you think they are.

I disagree that most of the ENCODE workers don't like junk DNA. On the contrary, I went through their words with a fine tooth comb, and not one advanced an argument or cited evidence against the Junk DNA hypothesis-- the one exception being Rule_30's statement about "good riddance" to Junk because it's been tending to get smaller. However, Rule_30 made that statement when he thought Larry was a Muggle (non-scientist). When he realized he was talking to a scientists, he edited his post and walked it back.

Later Rule_30 told us we can't call it "Junk DNA", but we can call it "Extra DNA", and believed he was defining "Extra" so that it appeared to be a different definition than (what he though was) the definition of "Junk". The problem is, his definition of "Junk DNA" was wrong, so, not knowing that, he defined "Extra" so it's practically the same as "Junk", while he believed it was different from "Junk."

Michael Hoffman said, depending on your definition of "function", the number should be between 5 to 80%. Way to be specific. But with that kind of vagueness, you can't disprove Junk DNA.

Rule_30 admitted that they define words in new ways in order to get money.

Rule_30: All I can say is that we have had long debates on almost everything and eventually someone always has to put their foot down and just make the best decision that they possibly can so we can move forward. If some of the ~400 of us had our way, we might still be debating on [how to begin experimenting]... I am a big proponent of agnosticism, but even I know that I can't live my whole career that way (and as a grad student, I sure hope it will be a career) -- if you sell yourself too short, nobody will believe any of your results or fund you.

So they oversold themselves to get money.

...at the end of it all, you have to take a leap and make the best, truest, but still most interesting statement that you have -- and sometimes you will miss the mark. But as long as you do your best to explain things and are honest about where the data, assumptions, and analysis came from (as we were), the truth will come out.

I take this as a tacit admission that they have two definitions of "function": the sexy definition used to get the attention of Muggles, and the elite definition, totally different, that they think they can transmit to the initiates into the Eleusinian mysteries. a11_msp thinks lying won't inhibit science, as long as the elites can figure out the truth (wink wink, nudge nudge).

Also, from Rule_30: If nothing else, this has been a very good lesson for me as a graduate student about how to present complex results: do we engage in a bit of rhetoric (and here, I still don't think the rhetoric was intentionally misleading or even meant as rhetoric at all) or do we undersell our results and make them seem useless?

So Rule_30 thinks it's either/or: either you make your work seem useless, or else you use "rhetoric."

A11_msp admitted one good thing about ENCODE and its hype was in generating buzz so as to get money.

A11_msp: And in fact, huge projects like this generate buzz that may justify future public spending on science, so I don't think assessing the ENCODE funding in the terms of non-funded R01s is fully relevant.

I left some long, angry remarks, accusing them of equivocating between two definitions of "function." No response yet.

One thing that's missing from the whole discussion is that the words "junk DNA" are nowhere to be found in the main integrative papers.

Also, it is ridiculous to claim that 442 scientists, some of them leaders in the fields of comparative and evolutionary genomics, don't know the literature on neutral processes which is so fundamental to those fields.

One thing that's missing from the whole discussion is that the words "junk DNA" are nowhere to be found in the main integrative papers.

I'm shocked as well. The entire ENCODE enterprise is about finding function yet none of the papers mention the competing scientific hypothesis. That's not good science, is it?

Also, it is ridiculous to claim that 442 scientists, some of them leaders in the fields of comparative and evolutionary genomics, don't know the literature on neutral processes which is so fundamental to those fields.

It would, indeed, be ridiculous if most of those scientists didn't understand evolution. Not looking good so far, however. None of the leaders have stepped forward to clarify the issues by showing that they fully understand the concept of junk DNA.

I wonder how many of these expects have read "The Origins of Genome Architecture" by Michael Lynch. Georgi, could you ask the members of your group and report back?

I read the whole REDDIT thread. None of them defined Junk DNA correctly. None of them seemed familiar with the positive arguments for Junk DNA. None seemed of them seemed to have given it any thought. They did, however, give a great deal of thought into how to generate buzz and funding by wrangling the media.

None of them could challenge the Junk DNA hypothesis with evidence-- Rule_30's "good riddance" comment was justified by the allegation that we're discovering new functions all the time, so it will go to zero. Which is a promise that they'll have the evidence some time in the future. Well, the newspapers trumpet that they have it now.

Yes, Ewan Birney announces to the newspapers that they have already crushed a hypothesis they call "Junk DNA" which they don't seem to understand. Strangely, they destroyed this hypothesis without ever citing (in the main ENCODE summary paper at least) the 1980 papers from Orgel and Crick nor Sapienza and Doolittle that described the hypothesis. As you know, Ewan Birney responded to the onion test by tweeting polyploidy.

At REDDIT, there was almost no understanding of positive arguments for Junk DNA, with two exceptions. There was a brief foray into why some genomes are bigger than others, leading to the coining of the term "Extra DNA" (new, good) which will now replace "junk DNA" (old, bad).

Rule_30: The simplest explanation I can think of right now would be that the smaller-genome pufferfish and larger-genome pufferfish have approximately the same genes AND regulatory elements, and that the larger-genome pufferfish has extra stuff that has nothing to do with gene regulation (I’m not prepared to dismiss it as “junk” DNA though). Assuming for a moment that this is true, and that humans have a similar amount or more of this “extra” DNA, I think it would still be possible to see the results that we see. What has a reproducible biochemical activity doesn’t necessarily have a biological function...

The genetic load argument was brought up and dismissed by hand-waving! Why, I guess the human species MUST be able to tolerate 150 new deleterious mutations per generation! After all, all DNA is "functional" now, right?

A11_msp: Personally, I don't think this changes our understanding of genetic load or genetic noise conceptually, it simply indicates that the system can probably tolerate much more genetic noise than was previously thought - even when such mutations show a clear evidence of a negative selective pressure.

A non-biologist published a simple population genetics equation that demolished this hand-waving. There was no response. Yes, non-biologists understand the math of population genetics better than the ENCODE spokesmen.

Larry, if I remember correctly Genomic sequencing of human populations shows that most of us harbor large deletions in our genomes yet we are quite healthy. Doesn't this show that many of those "functional" sites found by ENCODE are functionally irrelevant? Am I Confused?

Does anyone remember the arsen based lifeform? The study was published in Science and done by NASA?

I dare two prediction1) the 80% thing will be rejected by experimental studys (random genom project for example; I hope they are going to do this)2) the IDiots will cite the ENCODE papers to the end of time

They were pretty good at collecting the data. Not so good at interpreting the data. And excellent at prompting their false interpretations. In addition, they actually didn't filter their data to discriminate signal from noise. Alternatively they did but their filters didn't take reality into account.

If the likes of you and Moran have had time to read and really think about all of the ENCODE papers AND discuss your questions and concerns about the content of those papers with the co-authors and with other experts in the field (not other amateurs in the blogosphere), I don't know whether to be impressed or wonder how it is that you have nothing better to do with your time than rant about the brilliant efforts of others.

That's an extremely ignorant statement - ENCODE has invested HUGE amounts of time and statistical expertise and manpower into developing methods for dealing with signal/noise issues in NGS-based functional genomics analysis. That's in fact one of the biggest contributions of the project to the community. You can only say that if you have no idea what you're talking about

Another thing that puzzles me that even the way they define functional is questionable. ENCODE defines alterations of DNA or DNA associated proteins as biochemical functions (e.g. histone modifications). Correct me if I am wrong but don't they mess cause and effect? It's like claiming that a feature of a product of an enzyme reaction is its biochemcal function. IMO the product is just a read out for the biochemical function that resides in the enzyme.

There is a difference between collecting data and interpreting it.Creationists are often accused of denying the research work data in origin subjects because we disagree with the interpretation.In fact the geological presumption behind fossils determines the connections they draw.The fossils don't say anything but only interpretation of them goes on in these matters.

I thought the Luskin thing was quite good if sharp.He's not questioning motives but rather instincts all people have to back up favourite opinions. His last lines say this.

It is notable how much intellectual motives are said to be in play here as opposed to unbiased research. Likewise basic abilities .

Creationists would find things like this proving again how origin subjects are very open to human error by everyone's account.Its not like real sciences where error is eliminated through the standard of investigation.Origin subjects are complicated more so.

I agree. Now explain this to me. SInce there is a difference between collecting data and interpreting it, why is it that creationists such as the IDiots busy themselves quoting and misquoting abstracts rather than looking at the data?

Creationists are often accused of denying the research work data in origin subjects because we disagree with the interpretation

Nope, there is proper interpretation and then there's propaganda, such as the one propagated by creationists, such as the IDiots. As easily demonstrated, creationists don't look at the data, they either deny it or misquote.

Well, I stop here. You came just to present your usual creationist propaganda and stupid assertions.

I don't know the horse ebooks!Yet if its about horse evolution well its case in point.Horse fossils show no evolutionary process ever took place.All they show is fossils of different types of horses or creatures said to be the origins of horses.Yet the fossils say nothing but a snapshot of a dead creature.Its only, but only, a interpretation that this fossil evolved into that because of a GEOLOGICAL presumption that they were separated in time and enough time to allow one to become another.Without the geology there is NO evidence they evolved from each other.No biological evidence.They can easily be seen as just a diverse varity living in a richer world back in the day.People are not being persuaded that there was horse evolution from this fossil to that based on examining the fossils.Rather they are being persuaded about horse evolution from these fossils because of confidence in the geological conclusions.

Without the geology there is no biological conclusions to set up as evidence for evolution if horses are the topic.The horse fossils say nothing.the biology says nothing.The geology is saying everything.I say fossilism has nothing to do with biological investigation for the origins of biology.I say the geology is also plain wrong.all horse fossils were laid within weeks or moths of each other.Horse diversity was simply like modern amazon diversity.Its been a flawed logic and investigation.

I didn't have time for more than skimming through the ENCODE’s paper (distributing information over different threads may be fine for blogs but IMO it is not really convenient for scientific publications, but OK, ENCODE’s major driving force may have been the faith in SCIENCE 2.0, intentionally capitalized ) but another issue I think should be addressed is the cells ENCODE analyzed and the conclusion they derive from cell specific data. According to the ENCODE discussion on reddit besides one type of primary cells they only worked with cell lines (see the list at http://www.genome.gov/26524238) many of which are virally transformed or are known to carry chromosomal aberrations. Given ENCODE's assumption that most of the genome is functional how would they filter out the effects of e.g. EBV used to immortalize lymphocytes? What about cell lines that lack large parts of the normal set of chromosomes or trisomic for one or several chromosomes? E.g., according to ATCC the cell line K562 ENCODE used displays the following features:

The stemline chromosome number is triploid with the 2S component occurring at 4.2%. Fifteen markers (M1 and M(15)) occurred in nearly all S metaphases. Spontaneous non-specific dicentrics occurred, but rarely. Unstable markers were also rarely seen. The X was disomic, and N9 was nullisomic.

Irrespective of the discussion on Junk DNA, does ENCODE actually compensate for chromosomal aberrations? If nearly every part of the genome is important for the regulation of a cell's life what can we learn if large parts are missing? In addition, we know that many immortalized and cancer cell lines are de-regulated, i.e. they express genes that are not expressed in their non-mutated ancestors. Of course one may define de-regulation as a specific kind of regulation that differs from normal regulation but did ENCODE do this?To be fair, ENCODE had to limit its scope in some way. It’s somehow like the situation in the early 80s when much cell biological and cancer research was done with cell lines. However, since the late 80s journals were critical about work on cell lines and rather asked for results obtained with primary cells. Thus, ENCODE’s claims about findings obtained with many different cell types may be pre-mature. They may not qualify as artifacts but may be limited to certain cancerous or proliferative cell states which are only useful if proper wild type controls are available.

If you look at the main integrative paper, there is a supplementary spreadsheet with the number of base pairs covered by each assay in each cell line. You can compare K562 to more normal cell lines for which the same assays were done and see for yourself whether there is a large enough difference for what you said to be a serious and valid concern.

The choice of cell lines was the subject of a long discussion within ENCODE - the Tier1 cell lines could have been something like HeLa and K562 instead of GM12878 and K562 (with the later addition of H1-hESC), which is obviously an even worse scenario from your point of view. But there was the practical necessity of being able to grow whatever the chosen cell line is in huge quantities by multiple labs for the hundreds of assays to be done on it - that's much more difficult with primary cell lines.

Regarding chromosomal aberrations - when you do ChIP-seq, you always compare the ChIP to a control sample (either sonicated DNA or an IgG IP) because there are all sorts of artifacts and biases that can give you false positives if you don't have that (one of which is the number of copies of a given piece in the genome in your cell lines relative to the reference). So whatever the underlying ploidy, this has little to no influence on the typical analysis which aims at identifying binding sites of transcription factors. Now, obviously, there are things for which this matters - for example, if you're trying to look at allele-specific transcription factor binding or gene expression - but for most purposes it is not such a big concern and nobody is trying to do things that would be seriously confounded by this

Yes, hilarious. Luskin leaps to the defence of impugned 'Darwinists', and criticises critics for a perceived agenda. This from the man who thinks common design is a better explanation of sequence similarity than common descent. I'm sure he makes a bundle getting people off paternity suits with that one. Oh, of course, species boundaries. Forgot.

And he knows more about palaeontology than any palaeontologist, molecular biology than any molecular biologist, genetics than any ...

I predict this will become a running problem for science as the junkists fight both the creationists and take repeated aim at people who assert they've discovered function within the junk pile. Their giving aid and comfort to the enemy will become just another feature of this hundred-fifty years ideological war. Science held hostage.

There’s been a lot of talk at Sandwalk lately about the ENCODE consortium, a significant and massive scientific undertaking consisting of over 400 scientists. Much has already been said at Sandwalk to minimize any negative implications on the evolutionary view that (whether a little or a lot) so-called junk DNA is functional garbage left over from an evolutionary history. It seems even some Sandwalk fans fear projects like ENDODE and its potential to feed creationism. ENCODE has done several things, besides confirm that the human genome continuously reveals itself to be more sophisticated than even scientists ever imagined. For over a decade, Fazale Rana of Reasons To Believe has ‘predicted’ that discoveries in the human genome would point more to purposeful design than to random unguided natural selection. As a PhD biochemist, he has made those predictions in a scientific context (“The Cell's Design: How Chemistry Reveals the Creator's Artistry”), which ‘co-incidentally’ correspond to his personal beliefs as a Christian. ENCODE (probably constituted of naturalists and evolutionists) has confirmed Rana’s predictions by hammering one more nail in the coffin of the proposition of naturalistic evolution. Evolutionary theory lacks the essential element of predictability. It can only observe the obvious natural facts and postulate an a priory naturalist’s view. Creationism (of the old-earth/progressive variety) can make scientific predictions and enjoy seeing them confirmed by the facts or inferences of virtually every scientific discovery, like those of ENCODE. Larry once mentioned that he had a copy of Hugh Ross’ “Creation as Science” book, which has a table of comparative and implied predictions of future scientific discoveries, according to the major public views of natural science. I wonder if he would re-visit the Table titled, “Predictive Tests For Creation/Evolution Models (Complex Sciences)” and note which proposition (Creation/Evolution) has the best track record of predictability.

There were one or two mocking predictions made in this thread. I wonder if any qualified Sandwalk fan would venture a real scientific prediction about the human genome that would likely be verifiable in the short-term.

You can keep hammering your nails into the coffin, but there is no lid on it nor body inside! Many organisms have little or no junk DNA, as a matter of long-agreed fact. They include most prokaryotes, but also bats, birds and puffer fish. Indeed, prior to 1972 or so, no-one was expecting to find much of any organism's DNA to be non-functional. The ideas took a while to take hold, but they did, for valid reasons which appear to still hold true. It was certainly not taken up for ideological reasons, in support of some notion that the messier the genome, the more support 'naturalistic' evolution gained. Many of the strongest proponents of 'naturalistic' evolution were, indeed, decidely lukewarm about junk.

I'd have been really impressed if Creationism had predicted the pattern. As it is, they just said something vague - junk will turn out to have function, you mark our words. And no-one doubted that it would. How much might need to be reclassified in which organisms is still a long way from clear. Regardless of ENCODE, I would not hold out much hope for dead-transposon and virus sequence, so there's half your genome for a kick-off.

So, rewrite the history books if you wish. That's the great thing about predictions. If they are wrong, you simply never speak of them again. If correct - or even being sufficiently vaguely formulated that they may appear confirmed by new data - you can drag 'em out and crow like the morning cockerel. Creationists have no doubt that the ENCODE work is entirely accurate, including all interpretations, and 80% means 80% (at least). Yet every other paper by 'Darwinists' is sneered at by Luskin, Hunter, Rana et al. Confirmation bias, much?

Denny, I confidently predict that within a short time (about one year) real science will win and the ENCODE speculations will lose. The consensus among scientists will be that we do, indeed, have lots of junk in our genome.

If that happens, will you be willing to admit that Hugh Ross and his buddies were wrong?

Unfortunately, Denny, IDiot "predictions" are based purely upon ideology - what they imagine an intelligent designer would do. Scientific predictions are based upon knowledge and understanding of the natural world.

As could be forseen notorious <a href="http://www.huffingtonpost.com/james-a-shapiro/bob-dylan-encode-and-evol_b_1873935.html>James A. Shapiro</a> is claiming to have predicted the outcome of ENCODE's efforts in a paper he pulished together with Richard von Sternberg back in 2005.

I was not aware that Prof. Shapiro had coauthored a paper with Richard Sternberg (it is not clear that the von is in his given name). Sternberg is a creationist who was involved in a manufactured controversy with the Smithsonian Institute in Washington, D.C. It speaks poorly of Prof. Shapiro that he con-authors papers with nutcases like Sternberg.

Is there sth. wrong with the peer review process? We get ridiculous questions when trying to publish, but rarely I got questions thinking along the big lines concerning the hypothesis that was may be challenged. I feel there is sth. increasingly wrong with this system. The encode paper just one example.

Allan, the “nail in the coffin” is simply a cheerleading metaphor, as you know. It’s used because there’s a contest going on here, a contest of ideas, ideas that go beyond the science lab, and science is used as a referee by all sides. Many times at Sandwalk, people have said we don’t know everything and probably never will. In the mean time, unless you believe me wrong, predictability and inferences are key elements of the scientific method, and in the contest of ideas. Predictability and inferences contribute to scientific interpretation and the general discussion of what the details of natural science tell us, as they are revealed. That’s why (I think) Larry entered so many ENCODE posts lately - The project contains inferences.

Larry, Hugh Ross has often said (paraphrasing) that if science proved there was no god, he would give up his faith. It was actually a more succinct statement than that, but I don’t have the quote. If the natural universe itself is not a direct and specific revelation of God and His handiwork, with purposes that go beyond mere existence and observation, then I too would have to give up my faith. Meantime, we get to have the fun of being in this contest. And as with any contest, and as you said in your reply, there will be winners and losers. Speaking as a Christian, we don’t like the idea of being a loser, because we think losing has implications beyond a simple temporal disagreement. While it’s a pretty general prediction (Larry said, “real science will win and the ENCODE speculations will lose.”), and God willing I’m still around, I look forward to who claims to be the winner in a year.

Hugh Ross has often said (paraphrasing) that if science proved there was no god, he would give up his faith.

If Hugh Ross ever said such a thing, it proves his totally ignorant of science. There is no such thing as proof in science. Proof is a concept in mathematics and symbolic logic. In science, there is only evidence that supports a proposition or evidence that falsifies it. Has Prof. Ross ever described what sort of evidence would falsify the existence of god?

The position of atheists like Richard Dawkins is that they see no scientific evidence for the existence of god and therefore have concluded that it is unlikely that she exists. They have concluded that the hypothesis that god exists appears unnecessary as scientific materialism appears to provide sufficient explanations for what is observed.

Denny, the ENCODE data disprove the Junk DNA hypothesis, and the ENCODE workers themselves admitted it on the REDDIT thread. Why are you disputing their statements.

I'm going to copy and paste what I wrote on the REDDIT thread.

There has been a great deal of equivocating between different definitions of "function." An extremely broad definition that was used to get the 80% number.

However, no matter how you redefine "function", you cannot disprove the Junk DNA hypothesis with the ENCODE data as it now stands, simply by redefining words.

If you define "function" broadly, then most (80%?) of the human genome is "functional"-- but that is not relevant to the Junk DNA hypothesis, which uses a different, narrower definition of functional.

If you define "function" narrowly, that might be relevant to the Junk DNA hypothesis, but ENCODE's data do not show that most of the human genome is "functional" by that narrow definition.

For example: we are constantly told that ENCODE showed 76% of the genome is transcribed, maybe at low levels. This is most of the genome-- but it is not relevant to the Junk DNA hypothesis. When Junk DNA was defined back in the 1970's, the authors allowed for the possibility that much of it could be transcribed. This is very clear in David Comings' book from 1972; he knew that at least 25% of the mouse genome was transcribed, much more than the coding regions. This is nicely described in T. Ryan Gregory's comparison of Coming 1972 vs. ENCODE 2012, a must-read. The fact that we know 76% of the human genome is transcribed, sometimes at very low levels, does not disprove the arguments of those alleged dummies from the 1970's.

"Junk DNA" was never defined as "DNA whose function we don't know right now." It was certainly never defined as "non-coding DNA", and never defined as "DNA that is not transcribed."

For Sesumu Ohno, Junk meant pseudogenes. I think it changed over time. For the purposes of clarity, I'll define "Junk DNA" as "DNA that cannot suffer a deleterious mutation (at least not a point mutation.)"

Let's recap the false narrative now coming from the Muggle press, the pop-science press, and the creationists. Here's their story:

(1). Years ago, arrogant, ignorant scientists believed most human DNA was not "functional" only because they didn't know its "function."

(2). The ENCODE consortium proved that 80% of human DNA is "functional".

This "paradigm shift" narrative cannot possibly be true no matter what definition of "function" you choose. Re-defining "function" cannot make both (1) and (2) true in the same sense. There is no paradigm shift unless both (1) and (2) are true by the same definition of "function". So there is no paradigm shift.

If you use the Muggle definition of "function"-- that is, "involved in maintaining individuals’ well being", "serves some purpose", "plays critical roles" [these being actual phrases appearing in the New York Times, Washington Post etc.]-- then (1) is true but (2) is false. This definition is relevant to the Junk DNA hypothesis-- but you haven't disproven it, as ENCODE researchers have all admitted, right here on this REDDIT thread.

If you use the definition of "function" used to get the 80% number in the abstract of the ENCODE paper (the DNA is transcribed, or interacts with any biomolecule), then (2) is true but (1) is false. This definition is not relevant to the Junk DNA hypothesis. Scientists, years ago, never said that most human DNA was non-functional by your new, super-broad definition of "function."

Now I have two questions for you.

A. Do you agree that both (1) and (2) above cannot both be true by any single definition of "function"? That is, you have not produced any paradigm shift, and your data cannot disprove the Junk DNA hypothesis, where "Junk DNA" is defined as "DNA that cannot suffer a deleterious mutation"?

B. Do you agree that the non-scientist (Muggle) press and Intelligent Design movement has seriously misrepresented your results by alleging that you have disproved the Junk DNA hypothesis?

Please give me a straight answer to these two questions. They're not hard.

SLC,I tried to give myself a little wiggle room on Hugh’s remarks, which I have read and heard (while at a “Has Science Found God” conference a few years ago at the University of Toronto). If I can get the quote before this thread goes stale, I’ll offer it for you to critique. Until then, I’m sure you get the meaning. If science proved to be more reliable that the Bible, that would throw our faith into question.

Ya know, SLC. I dislike your ad hominem attacks. However, you were civil and specific enough recently to point out that your PhD thesis advisor was a “born again” Christian. You indicated that he was intelligent enough and capable in his understanding of physics sufficient to be your advisor (If I recollect correctly). But, you never indicated if you viewed him as an IDiot because of his faith. Was he a creationist of the theistic evolution type? Was he a young-earth’er? Was he a progressive creationist? In other words, how would you compare him to Hugh Ross, in the context of having scientific credentials as well as being a person of faith (In God)?

My PhD thesis adviser would be described as an old earth creationist (pretty hard for someone conducting research into elementary particle physics to believe in a young earth as he/she would have to reject quantum mechanics) who rejected common descent. However, my sense is that he knew next to nothing about the subject matter. Neither did I at the time.

By the way, Mr. Denny wouldn't like him very much because, despite being a born again Christian, he was pro-choice on abortion and supported the passing of a liberalized abortion law in New York State (this was before the Roe vs Wade decision in 1973).

Diogenes, Even if your figures were accurate, since when did science become a matter of majority rules? Before Galileo, the vast majority of the scientific establishment voted for a flat earth. Outside of your personal and parochial interests, how do you know that evolution isn’t the modern equivalent of a flat earth?

SLC, So. If you ran into your advisor tomorrow, and asked his opinion on common descent, and he gave you any answer other than undirected natural election, would that make him an IDiot? You know what I’m getting at. If you show respect for your theistic advisor, based on his education and credentials, why do show only disrespect for Hugh Ross, since it’s likely Ross and your advisor have more scientific and religious agreements than disagreements.

Further, It is for certain that your advisor and I would disagree over abortion. But he and I would know that those differences were settled at the foot of Christ’s Cross. He and I are spiritual brothers and I would indeed love him, as he would me.

SLC, So. If you ran into your advisor tomorrow, and asked his opinion on common descent, and he gave you any answer other than undirected natural election, would that make him an IDiot?

In the first place, Prof. Moran would take issue with the statement that only natural selection is responsible for evolutionary change. Genetic drift is also a driver of evolutionary change in his view. I personally have no opinion on the subject, not feeling competent to pontificate on the matter.

In the second place, if my former thesis adviser denied common descent, I would refer him to the video of Ken Miller which I have posted several times in response to Mr. Denny and to which he has thus far failed to respond to.

As a matter of fact, that video was sufficient to convince Prof. David Heddle, who has a PhD in nuclear physics and is also a born again Christian and teaches physics at Christopher Newport Un., in Newport News, VA. of the likelihood that common descent was a correct theory.

Sorry, SLC. I do have a life, which includes a wife, work (non scientific), wonderful grandkids, and a never-ending ‘to-do’ list. They often take priority over my viewing and reading everything available in the realm of natural science. If you’ll be so kind as to provide Ken Miller’s link once more, I’ll try to check it out and think about his proposition. Please don’t hold your breath for a quick response.

It probably won’t surprise me too much, if Prof. David Heddle (never heard of him) thinks “common descent was a correct theory.” These are immensely complex issues, and the evidence is not always definitive or conclusive. It also may not surprise me, based on what his previous views may have been.

Also, I’ve seen Larry mention and discuss genetic drift several times. Idon’t understand it, and I’m not disputing him. I simply use natural selection as a general term supporting the macro idea of Darwinian or neo-Darwinian undirected evolution.

The video with Ken Miller (no atheist he) is 4 minutes long. Surely Mr. Denny can spare 4 minutes out of his busy life to learn something about science for a change, rather more then he will learn from reading the rubbish put out by Hugh Ross and his followers. By the way, if Mr. Denny follows this blog, he will know that Prof. Moran is not a member of the Ken Miller marching and chowder society.

SLC said, “if Mr. Denny follows this blog, he will know that Prof. Moran is not a member of the Ken Miller marching and chowder society.” – I see that Larry disagrees with others in his and related fields of biological science. I enjoy the scientific contest, and struggle to sort out all the biases, which everyone claims do not exist.

Larry said: "Denny, I confidently predict that within a short time (about one year) real science will win and the ENCODE speculations will lose. The consensus among scientists will be that we do, indeed, have lots of junk in our genome"

I've been thinking about this and I think it will take a hell of lot longer than one year to undo the ENCODE hype. Consider that they've made a claim for 80% of the genome. Will there be another project that will examine a similar fraction and determine it has no real function ( as the term is commonly used) ? I think not. At best this claim will be chipped away at and it will take a LONG time before most reject it. As for how it can be chipped away at....perhaps looking at a region, such as the BRCA1 locus with a huge number of recent duplication,deletions and translocations and showing that ENCODE has it all annotated as 'funcional' Are there transcription factors that are known (from microarrays etc?) to have only one or a handfull of targets? If binding sites for that TF light up the genome we could say with confidence that almost all are functionless. Then there are ALU polymorphisms, gene deserts etc.... If I knew how to access the ENCODE info I'd make a stab at it but I dont have time to figure it out

I (Denny) made earlier comments about the ENCODE consortium, because I think its findings have implications that go beyond natural science to the innate longings of human beings and what the future holds. However, I know you have all been waiting to see what RTB’s Dr. Fuz Rana (PhD biochemistry) has to say about ENCODE’s findings, so here is his early interpretation.

“I (Fuz Rana) was asked to prepare a response to one of our high-end Donors who saw articles … and was concerned that ENCODE was no big deal. Below is what I wrote. I hope this is helpful.

“I have spent some time collecting the responses of the scientific community to the ENCODE project. By and large, there is a lot of excitement about their accomplishments and the potential for biomedical applications.

“The scientists who are dismissing the significance of the ENCODE findings (i.e. 80% of the human genome consists of functional elements) are, as far as I can tell, a vocal minority. I plan on writing an article detailing their complaints and offering a responseto their concerns.

“In my view, this vocal minority is engaged in some serious back peddling that has been prompted by creationists pointing out the apologetic significance of the ENCODE results.

“The two most common objections that have been offered up by the ENCODE “deniers” are 1) the results of the project have been hyped and poorly reported on by science journalists; and 2) the ENCODE scientists detected biochemical activity for 80% of the human genome and that it is incorrect to equate biochemical activity with function.

“As for the first point, I don’t think that the popular science reports represent hype at all. Nor do I think the science journalists, many who are among the best in the world, did a poor job on reporting on the results of the ENCODE project. For example, the ENCODE Project Consortium write in the abstract of the summary/overview article published in Nature (September 6, 2012) “These data enabled us to assign biochemical functions for 80% of the genome, in particular outside the well-studied protein-coding regions.” Sciencedaily.com published a news item on September 5, 2012 that is based on a press release issued by NIH/National Human Genome Institute in which Eric D. Green (Director of NHGRI) is quoted as saying, “During the early debates about the Human Genome Project, researchers had predicted that only a few percent of the human genome sequence encoded proteins, the workhorses of the cell, and the rest was junk. We now know that this conclusion was wrong.” Based on the paper’s abstract and this statement, it is hard to describe the reporting as being hype or poorly carried out.

“With regard to the second point, this represents a distinction without a difference, at least when it comes to the ENCODE study. The ENCODE project chose assays to specifically detect biochemical activity (transcription, binding of transcription factors, histone binding, sites where modified histones bind, methylation, and three-dimensional interactions between enhancers and genes) that biochemists know is functionally important for gene regulation and gene expression. The distinction between biochemical activity and function is a “slight of hand” and just a way to detract from what Christian apologists are saying about the significance of ENCODE. It is a tactic, nothing more.”

Denny, before you get too cocky you should consider the FACT that no matter what is found in a genome, it doesn't and won't verify that your imaginary god exists. Even IF the naturalistic theory of evolution is wrong in important ways, it doesn't and won't verify that your imaginary god exists. Even IF Larry is wrong, it doesn't and won't verify that your imaginary god exists.

To verify the existence of your imaginary god you need to provide substantial, testable, positive evidence. Do you have any?

And why did you pick the imaginary christian god? What about all the other imaginary gods people have dreamed up? Do you think that you would be a christian if you had been born and brought up in Iran?

What would you do if someone were to come up with solid evidence showing that Fifi the pink unicorn is the creator/designer, instead of your imaginary yhwh? Would you still believe in yhwh, or would you switch your beliefs and worship to Fifi?

Can you honestly say that there is more substantial, testable, positive evidence for yhwh than for Fifi? If someone were to say to you that they seriously believe in and worship Fifi the pink unicorn god and that Fifi is the one and only true god/creator/designer, how would you go about showing them that they are wrong and that you are right?

The Whole Truth said, – “they seriously believe in and worship Fifi the pink unicorn god and that Fifi is the one and only true god/creator…” - If they said that natural scientific evidence could support their Fifi belief, I would say, ‘show me where scientific data correlates or infers support for your belief.’ To infer is to take available data and deduce relatively compatible (i.e. non-contradictory, non-presumptive) conclusions based on that data. Evolutionists are typically evolutionarily presumptive in their view of natural science data. Layman like me, plus scientifically qualified Christians like Fuz Rana, can simply look at empirical data and deduce inference. That’s why the increasing level of sophistication and design characteristics revealed by scientific discoveries (i.e. supposed junk DNA, or not) infer a designer vs. an undirected unintelligent random natural force called evolution.

The same process can be applied to competition between gods. For example, if one looks at all the narrative creation accounts of all the religions, and compares them to known natural science data, even something as simple as the universe’s beginning, one would readily see that only the Bible’s creation account correlates to what is scientifically known about the universe’s beginning – in fact, that it had a beginning. No other religious holy books claim a beginning to the universe.

"... only the Bible’s creation account correlates to what is scientifically known about the universe’s beginning – in fact, that it had a beginning."

Well, it says that in the beginning God created the heaven and the earth, even before he created light. That doesn't match known scientific data at all (never mind the seven-day nonsense that follows). Then you are not even right about other religions being still less accurate. See e.g. the Vedic creation myth (Rigveda, Hymn 129). It's far better poetry than anything you can find in the Bible, and contains no "heaven and earth" BS. It would win your competition hands down if pitted against Genesis.

Piotr Gasiorowski said, “it says that in the beginning God created the heaven and the earth, even before he created light.” - A correct interpretation, using the original Hebrew word for "made" (asah) refers to an action completed in the past. Therefore, a correct interpretation is, "God had made" rather than "God made."

Also, the Hebrew phrase, "the heavens and the earth" (hashamayim we ha' erets) refers to the entire universe, entire creation and everything that can be seen or has physical existence. This indicates the heavenly bodies - the Earth, Sun, Moon, stars and other planets - were created "in the beginning" prior to the six creation "days," which represent eras or long periods of time.

Piotr Gasiorowski said, “you are not even right about other religions being still less accurate.” – Genesis is typically considered by Christian scholars as a historical or allegorical account, not poetry. As it relates to (Rigveda, Hymn 129), I am not familiar with it. I’ll leave it to you to translate and show how it correlates to a “beginning” or Big Bang event.

Denny: Therefore, a correct interpretation is, "God had made" rather than "God made."

The aspect makes little difference (English made can be interpreted as a perfective preterite, so the hair-splitting correction is simply unnecessary). The Biblical description is incompatible with scientific evidence no matter if the "days" are taken to last 24 hours or a hundred million years (I leave it to creationists to duke it out among themselves). If you interpret the passage literally, it's pure nonsense. If you insist on a metaphorical reading -- fine, but such a reading is unconstrained, hence arbitrary, subjective, and untestable.

As it relates to (Rigveda, Hymn 129), I am not familiar with it.

Here is the relevant fragment (translated by Ralph Griffith, 1889):

Darkness there was: at first concealed in darkness this All was indiscriminated chaos.All that existed then was void and form less: by the great power of Warmth was born that Unit.

Thereafter rose Desire in the beginning, Desire, the primal seed and germ of Spirit.Sages who searched with their heart's thought discovered the existent's kinship in the non-existent.

Transversely was their severing line extended: what was above it then, and what below it?There were begetters, there were mighty forces, free action here and energy up yonder.

Who verily knows and who can here declare it, whence it was born and whence comes this creation?The Gods are later than this world's production. Who knows then whence it first came into being?

He, the first origin of this creation, whether he formed it all or did not form it,Whose eye controls this world in highest heaven, he verily knows it, or perhaps he knows not.

At least you don't have to strain your imagination beyound reasonable limits to see a "strikingly accurate" description of the Big Bang here (I chose Griffith's Victorian translation deliberately, since he can't have heard about the Big Bang, and so his wording can't have been influenced by familiarity with modern cosmological models). Not that I regard the Vedic account as anything more than a piece of ancient myth, just like Genesis. With hindsight, just about any bloody thing can be read into such texts "allegorically".

One has to laugh at Mr. Denny. Many of the claims in the Hebrew bible have been discredited. For instance, archeological research has confirmed that the exodus from Egypt never happened. This is in addition to the totally ridiculous claim that the Hebrews wandered around in the Sinai Desert for 40 years. Since the distance from where the Suez Canal currently sits and the current border of Israel is about 100 miles, it could be covered in 2 weeks, even by a slow moving caravan. Therefore, if we are to believe the poppycock in the Hebrew Bible, the Hebrews must have been traveling in circles for 40 years! Totally preposterous.

Then, of course, there is the preposterous claim that Joshua stopped the Sun in the sky for a day. Aside from the fact that this would required violation of the laws of physics in order to prevent the consequences that would follow from such an event, there is not a jot or a tittle of evidence that anyone else in the world observed any such thing. It is beyond the realm of credibility that no one would have remarked on such an unusual occurrence.

Of course, there is the claim in the Christian bible that Yeshua of Nazareth was born of a virgin and had no earthly father. Scientifically, the only way this could be accomplished by humans would be if Mary was a hermaphrodite who impregnated herself/himself. Unfortunately, my information is that all human hermaphrodites have the male sex organs external, which would cause all sorts of physical difficulties for fertilization (I will cease and desist from describing these issues in clinical detail as this is a family blog).

Piotr Gasiorowski said, “The Biblical description is incompatible with scientific evidence.” - RTB takes a concordist view (Concordism = the book of nature and the book of scripture are telling the same story, though in different languages.) RTB expresses their view as a ‘Day-Age’ (a Day [English word translated from Hebrew] is commensurate with an Age/era of time. SLC seems to have a greater scholarship for judging ancient Hebrew language and interpreting scripture than me, so I’ll dispense with language and biblical interpretation and simply cut to the chase of what Genesis 1 is believed to say by RTB and old-earth creationists like me.

Genesis 1 is a chronological account of creation (Genesis 2 is a spiritual account of creation). Genesis’ 1 Day 1 was 4.5 bya. The moon and earth were formed; oceans became permanent. Day 2 was 3. to 2. bya. Blue-green algae dates to this period. Day 3 was 2 bya to 650 mya. Microorganisms and earth’s crust appear. Day 4 was 650 to 543 mya ‘possibly’ with first land plants. Day 5 was 543 to 65 mya with Cambrian explosion. Day 6 was 65 mya to about 50,000 years ago. Day 7 is not mentioned, because it is ongoing.

Piotr Gasiorowski said, “If you interpret the passage literally.” – An essential element of hermeneutics is that scripture should be taken in its plain sense unless there are compelling reasons to think otherwise. Genesis 1 is only one of at least twenty chapter length creation accounts in the Bible. When the respective contexts and best interpretations are taken into consideration for those twenty accounts, the Genesis 1 chronology I described above results.

Jud said, “Please name every other religious holy book ever written so we can verify you even are aware of them, let alone that you have assessed those religions/books for the absence of creation stories.” – Jud, what do you know that you did not learn from someone else, who learned from someone else, ad nauseam?

C'mon, Denny, the Biblical creation story is in the Old Testament, and is thus identical to the creation story of Christianity. So what makes Christianity different than Judaism in terms of being scientifically correct?

By the way, whatever you've heard or read is very, very wrong - virtually every religion you can think of has a creation story in its holy scriptures: Islam, Hinduism, Buddhism, and on and on.

Jud: Yes, we all recall the references to microorganisms and geology in Genesis.

They are ALLEGORICAL, you know. When God said "Let the earth bring forth grass, the herb yielding seed, and the fruit tree yielding fruit", he really meant "Let there be cyanobacteria yielding oxygen". It's the ABC of hermeneutics. And the next day he made the stars... oops, I mean by the next day he had made the stars, I'm sure that's what the Hebrew construction actually means. ;)

What you are doing is equivalent to what people do with horoscopes. The Bible has nothing about microbes, nothing about atoms, nothing about spherical Earths (though the greeks knew about it quite early in time), nothing that people of those times would not have known, and a lot of plainly imaginary shit. But, like people do with horoscopes you do with the Bible, you put a meaning there that is not really there. This is not "hermeneutics" (fancy word for making a fool of yourself), but "eisegesis" (putting a meaning into a text rather that situating yourself into the author's cultural and whatever else background: exegesis).

If you tried exegesis, instead of being erroneously bound into eisegesis, and thus investigated the cultural background of people's of those times and places, you would find an excellent correlation between what is said and quite the primitive superstitions and cosmologies. The Bible is a product of its times (with a good deal of tradition behind, but still a product of its time). It was written by people with no intervention by any super-omni-whatever gods.

As for the Ken Miller video, it is not as compelling as folks seem to think. First, it relies on a straw-man argument that non-Darwinists don't believe there has been genetic change in the human lineage. The chromosome fusion obviously occurred after the proposed human-chimp split. Is could have also occurred after God created humans separately with 24 pairs of chromosomes.

Secondly, the fusion is less clean than one would expect from a pure common descent argument. Consider the following evaluation of the fusion from Genome Research (http://genome.cshlp.org/content/12/11/1651.full.pdf+html)

"If the fusion occurred within the telomeric repeat arrays less than ∼6 Mya, why are the arrays at the fusion site so degenerate? The arrays are 14% diverged from canonical telomere repeats (not shown), whereas noncoding sequence has diverged <1.5% in the ∼6 Mya since chimpanzee and humans diverged"

No. It was an attack on "no common descent" creationism. Front-loaders, etc should not be bothered by this sort of thing at all.

... less clear than one would expect...

A few sources of this shocking variation. Oddly, I found them in the same paper;

"Overall, interspersed repeats occupy 40% of the sequence, with Short Interspersed Elements (SINEs) and Long Interspersed Elements (LINEs) accounting for 12% and 15% of the sequence, respectively."

and

"The AluYa5 and AluYb8 subfamilies have been transpositionally active very recently: 99% of the insertions of these elements are human specific, and ∼25% exhibit presence/absence polymorphism in humans"

and

"Interstitial arrays of degenerate telomere arrays are common in the human genome, particularly in subtelomeric regions (Riethman et al. 2001). Like the array at the fusion site, these arrays are highly diverged from the prototypic telomeric repeats (70% and 86% identical to [TTAGGG]n, respectively). A SATR1 (satellite) repeat cluster within the block common to 2qFus, 9pter, 9q13, and 9p11.2-B (asterisks in Fig. 3) also shows high variability in length, especially when compared with the overall high identity of these blocks."

and

"(2) The arrays were originally true terminal arrays that degenerated rapidly after the fusion. This high rate of change is plausible, given the remarkably high allelic variation observed at the fusion site."..."However, explanation 2 is supported by the high variability among allelic copies of other interstitial telomeric repeats and associated regions sequenced by Mondello et al. (2000) (AF236886 and AF236885)."

Miller's analysis only holds water if creationists discount the possibility of genetic change in humans. The fusion occurred exclusively (as far as we know) in the HUMAN line. One can quite easily accept both "no common descent" creationism and chromosome fusion.

The point in that paper is that it is not just a simple end-to-end fusion. At the very least, it is end-to-end fusion with a high rate of mutation/transposition.

The authors also present some troubling logic as to why this is human lineage only - the "F1 offspring would have had reduced fertility because of the risk of unbalanced segregation of chromosomes during meiosis." That problem would greatly reduce the probability of ANY descendents - humanish, chimpish or anywhere in-between - from the first common ancestor.

I am not a biologist or a geneticist so I am incompetent to comment on the paper presented. However, as I understand the issue, I would make the following observations.

The problem is that evolution makes a prediction that a fusion of 2 chromosomes must have occurred if apes and humans had a common ancestor. Creationism doesn't predict anything.

The second problem is that the split off the ape line resulted in the Australopithecus line, not the Homo line. Thus, the fusion could well have taken place before the Homo line split off from the Australopithecus line and probably did.

In addition, human chromosome 2 can be identified with ape chromosomes 12 and 13, with >98% identity.

The argument that IDiots like Casey Luskin are pushing is that the structures that Miller identifies as telomeres aren't really telomeres at all. This is repudiated by geneticists who, unlike Luskin, who doesn't know his posterior orifice from a hole in the ground, have been studying genetics for years

What's strange is that many could see the absurdity of the claims. So how did it get through peer review without being toned down? That might be the bigger problem that comes out of this fiasco.

The other alternative is that the journals knew this would lead to a big press release and publicity. This type of hype seems to be becoming more common. How often are editors overriding the objections of reviewers? Although, I can see this might be a good thing on a limited basis.

What worries me is that respectable journals such as Nature and Science Magazine are starting to look like the tabloid journalists of the science community. This is not the first time they have published papers where the priority is to generate news and publicity.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.